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Mapping gene expression in two Xenopus: evolutionary constraints and developmental flexibility

ABSTRACT: Mapping gene expression in two Xenopus: evolutionary constraints and developmental flexibility

PROVIDER: PRJNA137505 | ENA |

REPOSITORIES: ENA

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Mapping gene expression in two Xenopus: evolutionary constraints and developmental flexibility

Project description:Variation in gene expression is known to be important for morphological evolution, however little is known about its general propensity. Here we examine a pair of frogs M-bM-^@M-^S Xenopus laevis and Xenopus tropicalis M-bM-^@M-^S with highly similar embryology, and ask how their transcriptomes compare. Despite separation for over ~30-90 million years we found a strong conservation in gene expression in the vast majority of the expressed orthologs. There were a significant number of changes in the level of expression of genes. Changes in timing of expression, heterochrony, were much less common, and were often found in genes and pathways that reflect responses to selective features of the environment. Differences in gene expression levels were concentrated in the earliest embryonic stages. We propose that different evolutionary rates across developmental stages may be explained by the stabilization of cell fate determination pathways in later stages. 96 microarrays, across developmental stages in Xenopus laevis and Xenopus tropicalis in wildtype embryos. For each of the two timecourse indepenent triplicates (clutches) were generated.

2011-06-01 | E-GEOD-27227 | biostudies-arrayexpress

Mapping gene expression in two Xenopus: evolutionary constraints and developmental flexibility

Project description:Variation in gene expression is known to be important for morphological evolution, however little is known about its general propensity. Here we examine a pair of frogs – Xenopus laevis and Xenopus tropicalis – with highly similar embryology, and ask how their transcriptomes compare. Despite separation for over ~30-90 million years we found a strong conservation in gene expression in the vast majority of the expressed orthologs. There were a significant number of changes in the level of expression of genes. Changes in timing of expression, heterochrony, were much less common, and were often found in genes and pathways that reflect responses to selective features of the environment. Differences in gene expression levels were concentrated in the earliest embryonic stages. We propose that different evolutionary rates across developmental stages may be explained by the stabilization of cell fate determination pathways in later stages.

2011-06-01 | GSE27227 | GEO

Mapping gene expression in two Xenopus species: evolutionary constraints and developmental flexibility.

Project description: Not available

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Developmental constraints on behavioural flexibility.

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High-throughput laboratory evolution reveals global evolutionary constraints for antibiotic resistance

Project description:Understanding constraints which shape antibiotic resistance is key for predicting and controlling drug resistance. Here, we performed high-throughput laboratory evolution of Escherichia coli. The transcriptome, resistance, and genomic profiles for the evolved strains in 48 environments were quantitatively analyzed. By analyzing the quantitative datasets through interpretable machine learning techniques, the emergence of low dimensional phenotypic states within the 192 strains was observed. Further analysis revealed the underlying biological processes responsible for the distinct states. We also report a novel constraint which leads to decelerated evolution. These findings bridge the genotypic, gene expression, and drug resistance space, and lead to a comprehensive understanding of constraints for antibiotic resistance.

2020-10-12 | GSE137348 | GEO

Developmental constraints shape the evolution of the nematode mid-developmental transition

Project description:Evolutionary theory assumes that genetic variation is uniform and gradual in nature, yet morphological and gene expression studies have revealed that different life-stages exhibit distinct levels of cross-species conservation. In particular, a stage in mid-embryogenesis is highly conserved across species of the same phylum, suggesting that this stage is subject to developmental constraints, either by increased purifying selection or by a strong mutational bias. An alternative explanation, however, holds that the same ‘hourglass’ pattern of variation may result from increased positive selection at the earlier and later stages of development. To distinguish between these scenarios, we examined gene expression variation in a population of the nematode C. elegans using an experimental design that eliminated the influence of positive selection. By measuring gene expression for all genes throughout development in twenty strains, we found that variations were dramatically uneven throughout development, with a significant depletion during mid-embryogenesis. In particular, the family of homeodomain transcription factors, whose expression generally coincides with mid-embryogenesis, evolved under high constraint. Our data further shows that genes responsible for the integration of germ layers during morphogenesis are the most constrained class of genes. Together, these results provide the first evidence for developmental constraints as the mechanism underlying the hourglass model of animal evolution. Understanding the pattern and mechanism of developmental constraints provides a framework to understand how evolutionary processes have interacted with embryogenesis and led to the diversity of animal life on earth.

2017-04-04 | GSE87528 | GEO

Developmental gene expression of Xenopus laevis J strain [stage]

Project description:Comprehensive RNA-seq experiments to measure the expression of homoeologs across different developmental stages, as a part of the Xenopus laevis genome project. This work is funded by Agency Japanese Ministry of Education, Culture, Sports, Science and Technology (MEXT; "Genome Science" Grant ID 221S0002).

2016-10-24 | GSE73430 | GEO